Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of the bifunctionality of Marinobacter salinexigens ZYF650 glucosylglycerol phosphorylase in glucosylglycerol catabolism.
Journal, issue, pages	J Biol Chem, Vol. 301, Issue 2, Page 108127, Year 2025
Publish date	Dec 25, 2024
Authors	Di Lu / Keke Zhang / Chen Cheng / Danni Wu / Lei Yin / Quan Luo / Meiyun Shi / Honglei Ma / Xuefeng Lu /
PubMed Abstract	2-O-α-Glucosylglycerol (GG) is a natural heteroside synthesized by many cyanobacteria and a few heterotrophic bacteria under salt stress conditions. Bacteria produce GG in response to stimuli and ...2-O-α-Glucosylglycerol (GG) is a natural heteroside synthesized by many cyanobacteria and a few heterotrophic bacteria under salt stress conditions. Bacteria produce GG in response to stimuli and degrade it once the stimulus diminishes. Heterotrophic bacteria utilize GG phosphorylase (GGP), a member of the GH13_18 family, via a two-step process consisting of phosphorolysis and hydrolysis for GG catabolism. However, the precise mechanism by which GGP degrades GG remains elusive. We determined the 3D structure of a recently identified GGP (MsGGP) of the deep-sea bacterium Marinobacter salinexigens ZYF650, in complex with glucose and glycerol, α-d-glucose-1-phosphate (αGlc1-P), and orthophosphate (inorganic phosphate) at resolutions of 2.5, 2.7, and 2.7 Å, respectively. Notably, the first αGlc1-P complex structure in the GH13_18 family, the complex of MsGGP and αGlc1-P, validates that GGP catalyzes GG decomposition through consecutive phosphorolysis and hydrolysis. In addition, the structure reveals the mechanism of high stereoselectivity on αGlc1-P. Glu231 and Asp190 were identified as the catalytic residues. Interestingly, these structures closely resemble each other, indicating minimal conformational changes upon binding end-product glucose and glycerol, or the intermediate αGlc1-P. The structures also indicate that the substrates may follow a specific trajectory and a precise order toward the active center in close proximity and in a geometrically favorable orientation for catalysis in a double displacement mechanism.
External links	J Biol Chem / PubMed:39725037 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.5 - 2.75 Å
Structure data	61086 9j22 EMDB-61086, PDB-9j22: structure of human urea transport protein slc14A1 with urea Method: EM (single particle) / Resolution: 2.75 Å PDB-9j1u: Structural basis of the bifunctionality of M. salinexigens ZYF650T glucosylglycerol phosphorylase in glucosylglycerol catabolism Method: X-RAY DIFFRACTION / Resolution: 2.72 Å PDB-9j24: Structural basis of the bifunctionality of M. salinexigens ZYF650T glucosylglycerol phosphorylase in glucosylglycerol catabolism Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-9j25: Structural basis of the bifunctionality of M. salinexigens ZYF650T glucosylglycerol phosphorylase in glucosylglycerol catabolism Method: X-RAY DIFFRACTION / Resolution: 2.74 Å
Chemicals	ChemComp-GLC: alpha-D-glucopyranose ChemComp-GOL: GLYCEROL ChemComp-NA: Unknown entry ChemComp-G1P: 1-O-phosphono-alpha-D-glucopyranose ChemComp-HOH: WATER ChemComp-URE: UREA ChemComp-PLM: PALMITIC ACID ChemComp-PEG: DI(HYDROXYETHYL)ETHER ChemComp-TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH bufferYM ChemComp-PO4: PHOSPHATE ION ChemComp-SO4*: SULFATE ION
Source	homo sapiens (human) marinobacter salinexigens (bacteria)
Keywords	STRUCTURAL PROTEIN / Glucosylglycerol;phosphorylase-GH13_18;structure-double displacement mechanism / TRANSPORT PROTEIN / human urea transport protein slc14A1